Bioconductor Changelog

EBImage

fixed R CMD check memory leak (caused by a ReadImage() call after a drawtext() one); this was due to the MagickWandTerminus() destructor which also destroy MagickCore services (! see on ImageMagick wand/magick-wand.c for details)

metahdep

Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

Rintact

updated the list2matrix function and man page

chipseq

Deprecate most of the context functions (moved to
GenomicFeatures). The context distribution stuff is ported, but untested.

bgx

Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

yaqcaffy

yaqc.summary manual update
added summary(YAQCStatsObject) function

AnnotationDbi

adding to the TODO list

AnnotationDbi

Adds parameter for the inpIDMapper function.
This just adds another parameter so that you can choose to have the
final results limited to only one answer per initial ID even if you
map to something like a uniprot which may have many IDs for each
entrez gene ID. Default will still give you all of whatever you asked
for.
Added convenience function inpIDMapper
This function allows for easy mapping (using the appropriate
inparanoid packages) for IDs between species.

SemSim

Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

chipseq

some cleanup
changed interpretation of nsteps

LMGene

Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

chipseq

Another simulateReads rev.
Further speedup to simulateReads.
Further improvements to simulateReads function.
Improved performance of simulateReads.
Changed simulateReads function to use ShortReadQ class output

AnnotationDbi

This consolidates the INPARANOID_DB schemas into one.
By consolodating the INPARANOID schemas into one INPARANOID_DB schema,
I can now add more inparanoid packages without bloating up
AnnotationDbi any more than is strictly necessary...

chipseq

added alpha.hat to list of things computed

pdInfoBuilder

Prep'ing to add 2nd version of db-based annotation

AnnotationDbi

end of testing.
testing

SPIA

small bug fix and vignette update

chipseq

Adjusted the number of bins in the density calculations.

AnnotationDbi

Fixes a small bug in SQLForge and expands inpIDMapper.
This fixes a small bug where SQLForge fails when organsisms don't have
unigene IDs, and also expands the number of species that inpIDMapper
should work for.

pdInfoBuilder

Fixed merging of POS and NDF files

chipseq

one more mod
typo
one more set of tweaks
last piece
more updates to get the simulation code working

SPIA

updated pathway data by including interactions between genes and KEGG groups that contain at least one gene

AnnotationDbi

This adds support for worm, pig and chicken.
Adds code for planned support (October release) of these additional
organisms. These organisms are not supported at this moment.

RLMM

Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

EBImage

New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1

AnnotationDbi

Adds convenience function for listing .db0 packages.

AnnotationDbi

Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.

codetoolsBioC

Made error message more informative.
Stopped using ":::" operator since it doesn't support extraction from packages without namespaces.
Used Luke's suggestion to pass a modified collectUsageLeaf function into makeUsageCollector so the findGlobals search enters closures.
Recreate functions from scratch before passing to findGlobals function.

EBImage

Tried to provide a slightly more instructive warning when GTK+ cannot
be initialised at run-time.

GraphAT

Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

maanova

Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

CGHbase

Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

SPIA

Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

Rintact

Fixed Rintact dependencies so package will pass check.

macat

fixes for enabling HTML output with .db data packages

macat

Replaced usage of soon to be defunct class exprSet with ExpressionSet.

BicARE

This add BicARE, arrayMvout and affyContam to bioconductor.

cosmo

Fixed small bug in reverse complement calculation pointed out by Heejung

macat

fix to handle .db annotation packages

pdInfoBuilder

Cleaning up package, exporting only used classes
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.